Persistence and stability of generalized ribosome flow models with time-varying transition rates.
PLoS ONE, 2023 In this paper some important qualitative dynamical properties of generalized ribosome flow models are studied. Ribosome flow models known from the literature are generalized by allowing an arbitrary directed network structure between compartments, and by
Mihály A Vághy, Gábor Szederkényi
doaj +1 more source
The Gompertz model revisited and modified using reaction networks: Mathematical analysis
Biomath, 2021 In the present work we discuss the?usage of the framework of chemical reaction networks for the construction of dynamical models and their mathematical analysis.
Svetoslav Marinov Markov
doaj +1 more source
Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. [PDF]
PLoS ONE, 2012 Genome-scale network reconstructions are useful tools for understanding cellular metabolism, and comparisons of such reconstructions can provide insight into metabolic differences between organisms.
Joshua J Hamilton, Jennifer L Reed
doaj +1 more source
Challenges for Kinetics Predictions via Neural Network Potentials: A Wilkinson’s Catalyst Case
Molecules, 2023 Ab initio kinetic studies are important to understand and design novel chemical reactions. While the Artificial Force Induced Reaction (AFIR) method provides a convenient and efficient framework for kinetic studies, accurate explorations of reaction path
Ruben Staub +4 more
doaj +1 more source
The Smallest Multistationary Mass-Preserving Chemical Reaction Network [PDF]
Algebraic Biology, 2008 Biochemical models that exhibit bistability are of interest to biologists and mathematicians alike. Chemical reaction network theory can provide sufficient conditions for the existence of bistability, and on the other hand can rule out the possibility of
Anne Shiu
semanticscholar +1 more source
CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics [PDF]
Geoscientific Model Development, 2023 Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport.
H. Jung, H. Jung, H.-S. Song, C. Meile
doaj +1 more source
Prediction of Compound Synthesis Accessibility Based on Reaction Knowledge Graph
Molecules, 2022 With the increasing application of deep-learning-based generative models for de novo molecule design, the quantitative estimation of molecular synthetic accessibility (SA) has become a crucial factor for prioritizing the structures generated from ...
Baiqing Li, Hongming Chen
doaj +1 more source
Quantitative Propagation of Chaos in a Bimolecular Chemical Reaction-Diffusion Model [PDF]
SIAM Journal on Mathematical Analysis, 2019 We study a stochastic system of $N$ interacting particles which models bimolecular chemical reaction-diffusion. In this model, each particle $i$ carries two attributes: the spatial location $X_t^i\in \mathbb{T}^d$, and the type $\Xi_t^i\in \{1,\cdots,n\}$
Tau Shean Lim, Yulong Lu, J. Nolen
semanticscholar +1 more source
A continuous reaction network that produces RNA precursors
Proceedings of the National Academy of Sciences of the United States of America, 2020 Significance RNA may have been the original polymer to arise spontaneously on the early Earth through natural geochemistry. Although direct physical evidence regarding early Earth’s geochemistry is extremely limited, complex chemical reaction networks ...
Ruiqin Yi +6 more
semanticscholar +1 more source
A Theoretical Approach to the Complex Chemical Evolution of Phosphorus in the Interstellar Medium
The Astrophysical Journal, 2023 The study of phosphorus chemistry in the interstellar medium has become a topic of growing interest in astrobiology because it is plausible that a wide range of P-bearing molecules were introduced in the early Earth by the impact of asteroids and comets ...
Marina Fernández-Ruz +2 more
doaj +1 more source